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Asaia Spathodeae Sp. Nov., an Acetic Acid Bacterium in the Α-Proteobacteria

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Asaia Spathodeae Sp. Nov., an Acetic Acid Bacterium in the Α-Proteobacteria J. Gen. Appl. Microbiol., 56, 81‒87 (2010) Short Communication Asaia spathodeae sp. nov., an acetic acid bacterium in the α-Proteobacteria Jintana Kommanee,1 Somboon Tanasupawat,1,* Pattaraporn Yukphan,2 Taweesak Malimas,2 Yuki Muramatsu,3 Yasuyoshi Nakagawa,3 and Yuzo Yamada2,† 1 Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand 2 BIOTEC Culture Collection (BCC), National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand 3 NITE Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation (NITE), Kisarazu 292‒0818, Japan (Received July 23, 2009; Accepted September 14, 2009) Key Words—acetic acid bacteria; Asaia spathodeae sp. nov.; α-Proteobacteria; 16S rRNA gene restriction analysis The genus Asaia was fi rst described by Yamada et 2008a, b; Yukphan et al., 2004). The type strains of the al. (2000) with a single species, Asaia bogorensis, the three species were isolated respectively from fl owers type strain of which was isolated from the fl ower of an of the crown (Calotropis gigantea), heliconia (Helico- orchid tree (Bauhinia purpurea). Subsequently, Asaia nia sp.), and spider lily (Hymenocallis speciosa). siamensis, Asaia krungthepensis, and Asaia lannensis Strains classifi ed in the genus Asaia were character- were described (Katsura et al., 2001; Malimas et al., ized physiologically by no or weak oxidation of ethanol to acetic acid and by no or weak growth in the pres- ence of 0.35% acetic acid (v/v) (Yamada et al., 2000). * Address reprint requests to: Dr. Somboon Tanasupawat, Tanasupawat et al. (2009) found that the two isolates Department of Microbiology, Faculty of Pharmaceutical Sci- that were isolated from fl owers of the African tulip ences, Chulalongkorn University, 254 Phayathai Road, Wang- (Spathodea campanulata) constitute a new species in mai, Bangkok 10330, Thailand. the genus Asaia during the course of the systematic E-mail: [email protected] study of acetic acid bacteria isolated from the natural † JICA Senior Overseas Volunteer, Japan International Coop- eration Agency (JICA), Shibuya-ku, Tokyo 151‒8558, Japan; environment of Thailand. Professor Emeritus, Shizuoka University, Suruga-ku, Shizuoka In this paper, we propose the name of Asaia spatho- 422‒8529, Japan. deae sp. nov. to accommodate the two isolates as a Abbreviations: BCC, BIOTEC Culture Collection, National fi fth species of the genus Asaia. Center for Genetic Engineering and Biotechnology, National Two isolates, designated as isolate GB23-2T (= BCC Science and Technology Development Agency (NSTDA), 36458T = NBRC 105894T = PCU 307T) and isolate Pathumthani, Thailand; NBRC, NITE Biological Resource Cen- GB23-3 (= BCC 31374 = NBRC 105182 = PCU 308), ter, Department of Biotechnology, National Institute of Technol- were isolated by an enrichment culture approach us- ogy and Evaluation, Kisarazu, Japan; PCU, Pharmaceutical Sci- ences, Chulalongkorn University, Bangkok, Thailand. ing a glucose/ethanol/acetic acid medium, which was The DDBJ accession numbers for the 16S rRNA gene se- composed of 1.5% D-glucose (w/v), 0.5% ethanol (v/v), quences of isolates GB23-2T and GB23-3 are respectively 0.3% acetic acid (v/v), 0.8% peptone (w/v) and 0.5% AB511277 and AB469044. yeast extract (w/v) and which was adjusted at pH 3.5 82 KOMMANEE et al. Vol. 56 (Katsura et al., 2001; Yamada et al., 1999, 2000; Yuk- 31, 40, 48, 40, and 6% respectively to isolates GB23-2T phan et al., 2004). The isolates were maintained on and GB23-3 and the type strains of Asaia bogorensis, agar slants comprised of 2.0% D-glucose (w/v), 0.5% Asaia siamensis, Asaia krungthepensis, Asaia lannen- ethanol (v/v), 0.3% peptone (w/v), 0.3% yeast extract sis, and Acetobacter aceti (Table 1). The type strains of (w/v), 0.7% CaCO3 (w/v), and 1.5% agar (w/v). Asaia Asaia bogorensis, Asaia siamensis, Asaia krungthepen- bogorensis BCC 12264T (= NBRC 16594T), Asaia sia- sis, and Asaia lannensis gave the DNA-DNA related- mensis BCC 12268T (= NBRC 16457T), Asaia krung- ness levels of 21‒53% to the two isolates. The data thepensis BCC 12978T (= NBRC 100057T), Asaia lan- obtained indicated that the two isolates genetically nensis BCC 15733T (= NBRC 102526T), and Acetobacter constitute a new species in the genus Asaia. aceti NBRC 14818T were used for reference strains. Gene fragments specifi c for the 16S rRNA gene-en- Chromosomal DNA was prepared after Saito and coding regions of isolates GB23-2T and GB23-3 were Miura (1963). DNA base composition was determined amplifi ed by PCR, as described previously (Tanasupa- by the method of Tamaoka and Komagata (1984). wat et al., 2004; Yamada et al., 2000; Yukphan et al., DNA-DNA hybridization was performed by use of the 2004). Two primers used for PCR amplifi cation were photobiotin-labeling method with microplate wells, as 20F (5′-GAGTTTGATCCTGGCTCAG-3′; positions 9‒ described by Ezaki et al. (1989). A single-stranded and 27 by the Escherichia coli numbering system, acces- labeled DNA was hybridized with DNAs from test sion number V00348; Brosius et al., 1981) and 1500R strains in 2× SSC and 50% formamide at 48.0°C for (5′-GTTACCTTGTTACGACTT-3′; positions 1509‒1492). 15 h. The levels of DNA-DNA relatedness (%) were de- Amplifi ed 16S rRNA genes were directly sequenced termined colorimetrically (Verlander, 1992). The color with an ABI PRISM BigDye Terminator Cycle Sequenc- intensity was measured at A450 on a model VersaMax ing Ready Reaction kit on an ABI PRISM model 310 microplate reader (Molecular Devices, Sunnyvale, CA, Genetic Analyzer (Applied Biosystems, Foster, CA, USA). USA). For the direct sequencing, the following six The DNA G+C contents of isolates GB23-2T and primers were used: 20F, 1500R, 520F (5′-CAGCAGC GB23-3 were respectively 59.7 and 59.8 mol% with the CGCGGTAATAC-3′; positions 519‒536), 520R (5′-GT range of 0.1 mol% (Table 1). The data obtained were ATTACCGCGGCTGCTG-3′; positions 536‒519), 920F closely related to those of the type strains of Asaia bo- (5′-AAACTCAAATGAATTGACGG‒3′; positions 907‒ gorensis, Asaia siamensis, Asaia krungthepensis, and 926), and 920R (5′-CCGTCAATTCATTTGAGTTT-3′; Asaia lannensis (Katsura et al., 2001; Malimas et al., positions 926‒907). Multiple sequence alignments 2008a; Yamada et al., 2000; Yukphan et al., 2004). were performed for ca. 1,378 bases with the program When single-stranded and labeled DNAs from iso- CLUSTAL X (version 1.83, Thompson et al., 1997). lates GB23-2T and GB23-3 were hybridized with DNAs Gaps and ambiguous bases were eliminated from cal- from tested strains, the levels of DNA-DNA relatedness culation. Distance matrices for the aligned sequences were 100, 100, 27, 38, 43, 36, and 5% and 100, 100, were calculated by the two-parameter method of Table 1. DNA base composition and DNA-DNA relatedness of Asaia spathodeae isolates GB23-2T and GB23-3. DNA G+C DNA-DNA relatedness (%) of Labeled DNA from (mol%) 1234567 A. spathodeae isolate GB23-2T 59.7 100 100 27 38 43 36 5 A. spathodeae isolate GB23-3 59.8 100 100 31 40 48 40 6 A. bogorensis BCC 12264T 60.2a 21 28 100 56 59 46 8 A. krungthepensis BCC 12978T 60.3a 35 43 27 100 39 23 5 A. siamensis BCC 12268T 59.3a 41 53 22 38 100 34 6 A. lannensis BCC 15733T 60.8a 31 41 30 36 23 100 5 a Cited from Katsura et al. (2001), Malimas et al. (2008a), Yamada et al. (2000), and Yukphan et al. (2004). Abbreviations: 1, Asaia spathodeae isolate GB23-2T; 2, Asaia spathodeae isolate GB23-3; 3, Asaia bogorensis BCC 12264T; 4, Asaia krungthepensis BCC 12978T; 5, Asaia siamensis BCC 12268T; 6, Asaia lannensis BCC 15733T; 7, Acetobacter aceti NBRC 14818T. 2010 Asaia spathodeae sp. nov. 83 Kimura (1980). The phylogenetic trees based on 16S in Fig. 2, isolates GB23-2T and GB23-3 were complete- rRNA gene sequences were constructed by the neigh- ly distinguished by showing the Asp type of restriction bor-joining method (Saitou and Nei, 1987), the maxi- patterns in HpyAV digestion in spite of giving restric- mum-parsimony method (Felsenstein, 1983), and the tion patterns common to the type strains of some of maximum-likelihood method (Felsenstein, 1981) with the Asaia species examined in StyI, BsoJI, SnaBI, and the program MEGA (version 4.0; Tamura et al., 2007). HpaII digestions. In contrast, the type strains of the The confi dence values of individual branches in the four Asaia species represented the Ab type of restric- phylogenetic trees were determined by using the boot- tion patterns in HpyAV digestion. strap analysis of Felsenstein (1985) based on 1,000 The cellular fatty acid composition of isolates GB23- replications. Pair-wise 16S rRNA gene sequence simi- 2T and GB23-3 as well as the type strains of the four larities were calculated for 1,414 bases between phy- Asaia species was determined in cells grown on NBRC logenetically related strains. 804 agar at 30°C for 24 h. Methyl esters of cellular fatty The phylogenetic trees based on 16S rRNA gene acids were prepared and identifi ed according to the sequences, which were constructed by the above- instructions of the Microbial Identifi cation system mentioned three methods, showed that isolates GB23- (MIDI, Hewlett Packard, Palo Alto, CA, USA). The iso- T 2 and GB23-3 were located within the lineage of the lates contained unsaturated fatty acid of C18:1ω7c genus Asaia and formed an independent cluster from (67.5‒67.8%) and straight-chain fatty acid of C16:0 the type strains of the four known Asaia species (Fig. (9.1‒10.3%) as major components. The cellular fatty 1). However, the two isolates were related phyloge- acids profi les determined were similar to those of the netically to the type strain of Asaia siamensis with the type strains of the Asaia species (Table 2).
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